[petsc-users] Out of memory and parallel issues

Matthew Knepley knepley at gmail.com
Thu Jan 1 00:06:19 CST 2015

On Wed, Dec 31, 2014 at 11:20 PM, TAY wee-beng <zonexo at gmail.com> wrote:

> Hi,
> I used to run my CFD code with 96 procs, with a grid size of 231 x 461 x
> 368.
> I used MPI and partition my grid in the z direction. Hence with 96 procs
> (8 nodes, each 12 procs), each procs has a size of 231 x 461 x 3 or 231 x
> 461 x 4.
> It worked fine.
> Now I modified the code and added some more routines which increases the
> fixed memory requirement per procs. However, the grid size is still the
> same. But the code aborts while solving the Poisson eqn, saying:
> Out of memory trying to allocate XXX bytes
> I'm using PETSc with HYPRE boomeramg to solve the linear Poisson eqn. I am
> guessing that now the amt of memory per procs is less because I added some
> routines which uses some memory. The result is less memory available for
> the solving of the Poisson eqn.

I would try GAMG instead of Hypre. It tends to be memory light compared to

  -pc_type gamg



> I'm now changing to KSPBCGS but it seems to take forever. When I abort it,
> the error msg is:
> Out of memory. This could be due to allocating
> [10]PETSC ERROR: too large an object or bleeding by not properly
> [10]PETSC ERROR: destroying unneeded objects.
> [10]PETSC ERROR: Memory allocated 0 Memory used by process 4028370944
> [10]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
> I can't use more procs because some procs will have a size of 231 x 461 x
> 2 (or even 1). This will give error since I need to reference the nearby
> values along the z direction.
> So what options do I have? I'm thinking of these at the moment:
> 1. Remove as much fixed overhead memory per procs as possible so that
> there's enough memory for each procs.
> 2. Re-partition my grid in both x,y direction or x,y,z direction so I will
> not encounter extremely skew grid dimensions per procs. Btw, does having
> extremely skew grid dimensions affect the performance in solving the linear
> eqn?
> Are there other feasible options
> --
> Thank you.
> Yours sincerely,
> TAY wee-beng

What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20150101/2b8c32be/attachment.html>

More information about the petsc-users mailing list